Characterization of porcine polymorphic microsatellite loci

Twenty-seven (CA)_n and two (GA)_n microsatellite clones were isolated out of a size-selected genomic pig library. These were sequenced and the number of uninterrupted dinucleotides was found to range from 12 to 26. Flanking primers were chosen for 11 dinucleotide repeats and optimal conditions for polymerase chain reaction (PCR) amplifications were established. Different microsatellite loci were amplified simultaneously by combining primer sets. Related and unrelated pigs were screened for length polymorphisms of the different microsatellite loci. The polymorphic information content (PIC) of these loci ranged between 0.62 and 0.83. Segregation studies in pig reference families established Mendelian inheritance. Locus S0022 was found to be X-linked.     

Isolation, characterization and cross-amplification of polymorphic microsatellite loci in the threatened endemic Mammillaria crucigera (Cactaceae)

The cactus Mammillaria crucigera is a threatened species endemic to central Mexico. As a means of assessing population genetic status of these species, eight microsatellite markers were developed. These primers were tested in 40 individual from two wild populations. The results showed that these primers will be useful to describe population structure and aid to the conservation of species. The eight primers were tested in other Mammillaria species and most of them showed successful amplification.     

Characterization of polymorphic microsatellite loci in Yucca filamentosa

Yuccas and their pollinator moths are a textbook example of mutualism, yet we lack sufficiently variable markers to properly study the population genetics of the plants. We characterized 13 polymorphic microsatellite loci for Yucca filamentosa by screening primers derived from an expressed sequence tag database. We found four to 13 alleles per locus and the observed heterozygosity ranged from 0.31 to 1. These markers will be useful in future ecological studies of Y. filamentosa.     

Characterization of polymorphic microsatellite loci in the marine isopod Sphaeroma terebrans (Crustacea, Isopoda)

Nine polymorphic microsatellites were characterized in the marine isopod Sphaeroma terebrans (Isopoda, Sphaeromatidae) for phylogeographic and parentage analyses. The number of alleles ranged from 3 to 10. Observed heterozygosity ranged from 0.428 to 0.950, while expected heterozygosity ranged from 0.532 to 0.889. Heterozygote deficiency was detected for one locus, possibly the result of null alleles.     

Characterization of polymorphic microsatellite loci in Castelnau's Antshrike,Thamnophilus cryptoleucus (Aves: Thamnophilidae)

In order to study the biogeography and population genetic structure of the obligate river‐island species Thamnophilus cryptoleucus (Thamnophilidae) we isolated four microsatellite loci. Number of alleles ranged from six to 11, heterozygosities from 60% to 89%, and individual populations were found in Hardy–Weinberg equilibrium. Cross‐species amplification of the loci was tested in eight species of the family Thamnophilidae and all loci successfully amplified in five or more related species.     

Characterization of 12 polymorphic microsatellite loci for eastern chipmunks (Tamias striatus)

Eastern chipmunks are small forest rodents for which ecological data at multiple spatial scales exist, but no molecular markers have been developed that provide adequate resolution to examine genetic structure at fine scales in this species. Thus, we developed 12 variable microsatellite loci, which amplified in three multiplexed reactions, and screened them in 27 individuals from northern Indiana, USA. Observed heterozygosities across loci ranged from 0.26 to 0.91 and number of alleles per locus ranged from three to 10. We will use these markers along with ecological data to understand population dynamics of eastern chipmunks at small spatial scales.     

Characterization of seven polymorphic microsatellite loci in the Common Loon (Gavia immer)

We describe polymerase chain reaction (PCR) primers and conditions to amplify seven microsatellite DNA loci isolated from the Common Loon (Gavia immer). The PCR primers were tested on 83 individuals from 10 locations in North America, including breeding, migration stopover, and wintering areas. Between two and seven alleles were observed to segregate at the seven microsatellite loci, with observed heterozygosities ranging from 0.048 to 0.695.     

Characterization of nine polymorphic microsatellite loci in the fungus Botrytis cinerea (Ascomycota)

Nine microsatellite markers were characterized in the fungus Botrytis cinerea. Genomic DNA sequences from the partial sequencing of 12 000 bacterial artificial chromosome (BAC) clones, were screened by BLAST for various microsatellite motives, and primer pairs were designed. Cross‐amplification and polymorphism were assessed on 49 isolates from B. cinerea and two related species, collected from natural populations on several plants and locations.     

Characterization of 8 polymorphic microsatellite loci in the neotropical ant-garden ant, Camponotus femoratus (Fabricius)

Camponotus femoratus is an abundant and behaviorally dominant ant in lowland Amazonian rainforests, where this species participates in a complex and obligate seed-dispersal mutualism. C. femoratus typically cohabits with another ant species Crematogaster levior in an apparently amiable but poorly understood interaction. Despite these outstanding characteristics, the population genetics and dispersal patterns of C. femoratus are unknown. We isolated eight polymorphic microsatellite loci for C. femoratus from a genomic library enriched for di-, tri-, and tetra-nucleotide repeats. We detected 2 to 17 alleles per locus, with levels of observed heterozygosity ranging from 0.286 to 0.714.     

Characterization of polymorphic microsatellite loci from black grouper,Mycteroperca bonaci (Teleostei: Serranidae)

Many groupers in the western Atlantic are vulnerable to overfishing, and appropriate management requires knowledge of the population structure of these fish. To this end microsatellite markers were developed from black grouper, Mycteroperca bonaci, using an enrichment procedure. Five loci with levels of polymorphism ranging from 0.5 to 0.9 were selected. These markers also proved to be useful in scamp, M. phenax; red grouper, Epinephelus morio; and goliath grouper, E. itajara. Conformation to Hardy–Weinberg equilibrium was observed except for heterozygote deficiencies noted for E. morio at two of the loci used for this species.     

Characterization of polymorphic tetranucleotide microsatellite loci from the Siberian weasel (Mustela sibirica)

Nine tetrarepeat microsatellite loci for Siberian weasel (Mustela sibirica) were characterized. By using 35 individuals of unknown relationship collected from Taiwan, we evaluated the polymorphism of these loci. The number of alleles for each locus ranged from five to 12 (mean = 8.78 alleles) and the observed heterozygosity from 0.429 to 0.962 (mean = 0.688) and all loci conformed to Hardy–Weinberg expectation.     

Characterization of 42 polymorphic microsatellite loci in Mimulus ringens (Phrymaceae) using Illumina sequencing

• Premise of the study: Microsatellite markers were isolated and characterized in Mimulus ringens (Phrymaceae), a herbaceous wetland perennial, to facilitate studies of mating patterns and population genetic structure. • Methods and Results: A total of 42 polymorphic loci were identified from a sample of 24 individuals from a single population in Ohio, USA. The number of alleles per locus ranged from two to nine, and median observed heterozygosity was 0.435. • Conclusions: This large number of polymorphic loci will enable researchers to quantify male fitness, patterns of multiple paternity, selfing, and biparental inbreeding in large natural populations of this species. These markers will also permit detailed study of fine-scale patterns of genetic structure.     

Characterization of polymorphic microsatellite loci for the invasive monk parakeet (Myiopsitta monachus)

Microsatellite loci were characterized for the monk parakeet (Myiopsitta monachus) from a GT_n‐enriched genomic library. Twelve of 14 microsatellite loci were polymorphic, averaging 6.7 alleles per locus across the 20 individuals genotyped. Mean expected heterozygosity was 0.72, with locus‐specific values ranging from 0.53 to 0.90. An equally high multilocus probability of identity (2.48 × 10^?12) was revealed for this set of loci. In addition, all 12 loci were demonstrated to cross‐amplify to varying extents within three additional parrot genera suggesting their potential utility for population‐level studies in a broad range of Neotropical psittacines.     

Development and characterization of microsatellite loci in endangered Astrophytum asterias (Cactaceae)

We report the development of polymorphic microsatellite markers for the endangered North American cactus Astrophytum asterias (Cactaceae). Six loci, averaging 8.5 alleles per locus, were found to amplify genomic DNA consistently in 94 individuals from four geographically defined demes in South Texas. These markers will permit the generation of appropriate data for estimating population genetic parameters, population structure and the degree of inbreeding in the small, fragmented populations of A. asterias that currently exist. These are the first microsatellites reported for the genus Astrophytum and for the tribe Cacteae.     

New chromosome counts and evidence of polyploidy in Haageocereus and related genera in tribe Trichocereeae and other tribes of Cactaceae

Chromosome numbers for a total of 54 individuals representing 13 genera and 40 species of Cactaceae, mostly in tribe Trichocereeae, are reported. Five additional taxa examined belong to subfamily Opuntioideae and other tribes of Cactoideae (Browningieae, Pachycereeae, Notocacteae, and Cereeae). Among Trichocereeae, counts for 35 taxa in eight genera are reported, with half of these (17 species) for the genus Haageocereus. These are the first chromosome numbers reported for 36 of the 40 taxa examined, as well as the first counts for the genus Haageocereus. Both diploid and polyploid counts were obtained. Twenty nine species were diploid with 2n=2x=22. Polyploid counts were obtained from the genera Espostoa, Cleistocactus, Haageocereus, and Weberbauerocereus; we detected one triploid (2n=3x=33), nine tetraploids (2n=4x=44), one hexaploid (2n=6x=66), and three octoploids (2n=8x=88). In two cases, different counts were recorded for different individuals of the same species (Espostoa lanata, with 2n=22, 44, and 66; and Weberbauerocereus rauhii, with 2n=44 and 88). These are the first reported polyploid counts for Haageocereus, Cleistocactus, and Espostoa. Our counts support the hypothesis that polyploidy and hybridization have played prominent roles in the evolution of Haageocereus, Weberbauerocereus, and other Trichocereeae.     

Characterization of polymorphic microsatellite loci in cultivated and wildPanax ginseng

Ginseng (Panax ginseng) is one of the most important herbal remedies used in East Asia. The present study investigated six polymorphic microsatellite markers (PG29, PG281, PG287, PG668, PG1319, and PG1481) in samples of cultivated and wildP. ginseng collected in Korea. Total allelic number observed in this study was 27 (average allelic numbers per locus: 4.5). All examined loci exhibited deviation from the Hardy-Weinberg equilibrium and deficiency of heterozygosity in both cultivated and wild groups. Although the wild ginseng group exhibited slightly more polymorphic behavior (mean PIC=0.392, GD=0.454 and H_obs=0.129), compared with the cultivated group (mean PIC=0.383, GD=0.438 and H_obs=0.105), no significant differences of allele frequencies and genotype distributions were revealed. By combined analysis of six loci in 100 cultivated ginsengs, 71 different types were observed. The analyzed microsatellite loci in this study will be helpful for understanding genetic variation, QTL mapping and phylogenic studies inPanax species.     

Characterization of eight polymorphic microsatellite loci for the giant grouper (Epinephelus lanceolatus Bloch)

Eight polymorphic microsatellite loci were isolated and characterized using a small insert genomic DNA library for the giant grouper (Epinephelus lanceolatus Bloch, 1790), a commercially valuable marine fish in tropical waters. They showed polymorphism information content ranging from 0.177 to 0.775, allele numbers ranging from two to 10, effective allele numbers ranging from 1.227 to 5.012, and observed and expected heterozygosities from 0.2 to 0.733 and from 0.185 to 0.801, respectively, which we anticipate will be useful for population genetic studies of the giant grouper.     

Characterization of polymorphic microsatellite loci in the aphid species Macrosiphum euphorbiae (Hemiptera: Aphididae)

Fourteen microsatellite loci were isolated and characterized in the potato aphid, Macrosiphum euphorbiae Thomas, by screening a genomic library with the oligonucleotide probes (GA)₁₀ (GT)₁₀ and (GATA)₄. Allelic diversity was estimated in samples collected from potato fields in Tunisia. Ten loci displayed polymorphism that ranged from two to four alleles per locus and the observed heterozygosity ranged from zero to one. These markers could be used to study the population genetic structure of this polyphagous aphid species.